Buggy code:
public class Main { public static void main ( String [ ] args ) throws FileNotFoundException , InterruptedException , ExecutionException { String filepath = "//home//peeyush//Desktop//genes.csv" ; System . out . println ( filepath ) ; String addQuery = "" ; <START_BUG> int maxAbs = 50 ; <END_BUG> int perRun = 50 ; int synonym = 0 ; int human = 1 ; int mouse = 0 ; int thread = 4 ; float Ethreshold = ( ( float ) ( 0.3 ) ) ; float Pthreshold = ( ( float ) ( 0.05 ) ) ; String test = "fisher" ; boolean pathway = true ; for ( int i = 0 ; i < ( args . length ) ; i ++ ) { String [ ] parameter = args [ i ] . split ( "=" ) ; if ( parameter [ 0 ] . contains ( "filepath" ) ) { filepath = parameter [ 1 ] . trim ( ) ; } if ( parameter [ 0 ] . contains ( "addQuery" ) ) { addQuery = parameter [ 1 ] . trim ( ) ; } if ( parameter [ 0 ] . contains ( "maxAbs" ) ) { maxAbs = Integer . parseInt ( parameter [ 1 ] . trim ( ) ) ; } if ( parameter [ 0 ] . contains ( "perRun" ) ) { perRun = Integer . parseInt ( parameter [ 1 ] . trim ( ) ) ; } if ( parameter [ 0 ] . contains ( "synonym" ) ) { synonym = Integer . parseInt ( parameter [ 1 ] . trim ( ) ) ; } if ( parameter [ 0 ] . contains ( "mouse" ) ) { mouse = Integer . parseInt ( parameter [ 1 ] . trim ( ) ) ; human = 0 ; } if ( parameter [ 0 ] . contains ( "Pthreshold" ) ) { Pthreshold = Float . parseFloat ( parameter [ 1 ] . trim ( ) ) ; } if ( parameter [ 0 ] . contains ( "test" ) ) { test = parameter [ 1 ] . trim ( ) ; } if ( parameter [ 0 ] . contains ( "thread" ) ) { thread = Integer . parseInt ( parameter [ 1 ] . trim ( ) ) ; } } if ( filepath == null ) { throw new FileNotFoundException ( "Please<seq2seq4repair_space>provide<seq2seq4repair_space>path<seq2seq4repair_space>to<seq2seq4repair_space>genename.csv" ) ; } FindDirectoryAddress createDir = new FindDirectoryAddress ( ) ; createDir . getpath ( ) ; ReadTextFile read ; List < String > new_all_genes = new ArrayList < > ( ) ; List < String > synonyms = new ArrayList < > ( ) ; List < String > all_genes = new ArrayList < > ( ) ; List < String > queries = new ArrayList < > ( ) ; TreeMap < String , ArrayList > abstracts = new TreeMap < > ( ) ; List < TreeMap < String , ArrayList > > abnerResults = new ArrayList < > ( ) ; TreeMap < String , ArrayList > abnerResult = new TreeMap ( ) ; List < String > entities2compare = new ArrayList < > ( ) ; ArrayList < Occurrenceobj > occurrenceResult = new ArrayList ( ) ; System . out . println ( "Check<seq2seq4repair_space>point:<seq2seq4repair_space>1" ) ; read = new ReadTextFile ( ) ; all_genes = read . extract ( filepath ) ; System . out . println ( all_genes ) ; CheckSynonymes cSynonym = new CheckSynonymes ( all_genes ) ; if ( synonym == 1 ) { System . out . println ( "Synonyms<seq2seq4repair_space>are<seq2seq4repair_space>being<seq2seq4repair_space>considered" ) ; if ( human == 1 ) { read = new ReadTextFile ( ) ; synonyms = read . extract ( ( ( FindDirectoryAddress . dirPath ) + "//resources//Human_synonym.csv" ) , "," ) ; new_all_genes = cSynonym . withSynonym ( synonyms ) ; System . out . println ( ( "Size<seq2seq4repair_space>of<seq2seq4repair_space>Human<seq2seq4repair_space>synonym<seq2seq4repair_space>list:<seq2seq4repair_space>" + ( new_all_genes . size ( ) ) ) ) ; } if ( mouse == 1 ) { read = new ReadTextFile ( ) ; synonyms = read . extract ( ( ( FindDirectoryAddress . dirPath ) + "//resources//Mouse_synonym.csv" ) , "," ) ; new_all_genes = cSynonym . withSynonym ( synonyms ) ; System . out . println ( ( "Size<seq2seq4repair_space>of<seq2seq4repair_space>Mouse<seq2seq4repair_space>synonym<seq2seq4repair_space>list:<seq2seq4repair_space>" + ( new_all_genes . size ( ) ) ) ) ; } cSynonym . WriteSynonyms ( synonyms ) ; } else { new_all_genes = all_genes ; } System . out . println ( "Check<seq2seq4repair_space>point:<seq2seq4repair_space>2" ) ; System . out . println ( "Check<seq2seq4repair_space>point:<seq2seq4repair_space>3" ) ; System . out . println ( new_all_genes ) ; String additionalQ = addQuery ; System . out . println ( addQuery . isEmpty ( ) ) ; if ( ! ( additionalQ . isEmpty ( ) ) ) { if ( additionalQ . contains ( "," ) ) { String [ ] adds = additionalQ . split ( "," ) ; List < String > qWords = Arrays . asList ( adds ) ; for ( String gene : new_all_genes ) { StringBuilder queryBuider = new StringBuilder ( ) ; if ( ! ( qWords . isEmpty ( ) ) ) { queryBuider . append ( gene ) ; for ( String q : qWords ) { queryBuider . append ( "<seq2seq4repair_space>AND<seq2seq4repair_space>" ) . append ( q ) ; } queries . add ( queryBuider . toString ( ) ) ; } else { queries . add ( gene ) ; } } } else { for ( String gene : new_all_genes ) { StringBuilder queryBuider = new StringBuilder ( ) ; queryBuider . append ( gene ) . append ( "<seq2seq4repair_space>AND<seq2seq4repair_space>" ) . append ( additionalQ ) ; queries . add ( queryBuider . toString ( ) ) ; } } } else { for ( String gene : new_all_genes ) { queries . add ( gene ) ; } }

Fix:
int maxAbs = 100 ;